Appl Microbiol Biotechnol DOI 10.1007/s00253-015-6903-8 MINI-REVIEW Omics on bioleaching: current and future impacts Patricio Martinez1 & Mario Vera2 & Roberto A. Bobadilla-Fazzini1 Received: 11 June 2015 /Revised: 27 July 2015 /Accepted: 30 July 2015 # The Author(s) 2015. This article is published with open access at Springerlink.com Abstract Bioleaching corresponds to the microbial-catalyzed Introduction process of conversion of insoluble metals into soluble forms. As an applied biotechnology globally used, it represents an The simultaneous study of the complete set of genetic, protein, extremely interesting field of research where omics techniques and metabolic material of living things will probably lead can be applied in terms of knowledge development, but more- science to decipher at least some of the mysteries of life. As over in terms of process design, control, and optimization. In genomics is not the only responsible for life’s complexity, this mini-review, the current state of genomics, proteomics, more B-omes^ are required to solve this puzzle (Ball 2013), and metabolomics of bioleaching and the major impacts of and therefore, we must account for the Bdark matter^ of the these analytical methods at industrial scale are highlighted. biological universe (Varki 2013). Bioleaching, known as the In summary, genomics has been essential in the determination microbial-catalyzed process of conversion of insoluble metal of the biodiversity of leaching processes and for development sulfides into soluble forms, has introduced the classical geno- of conceptual and functional metabolic models. Proteomic mics for a while, as well as the dark matter omics, such as impacts are mostly related to microbe-mineral interaction proteomics and metabolomics more recently, with great ad- analysis, including copper resistance and biofilm formation. vances in knowledge and several more to be accomplished. Early steps of metabolomics in the field of bioleaching have During the 1940s, the phenomenon of metal sulfide disso- shown a significant potential for the use of metabolites as lution in an acidic medium was first attributed to the action of industrial biomarkers. Development directions are given in certain microorganisms (Colmer and Hinkle 1947). This was order to enhance the future impacts of the omics in the first step in applying microbiology to mining and opened biohydrometallurgy. the door for research in acidophilic microorganisms among this field. Decades after this breakthrough, recovery of metals from sulfide ores employs several different types of Keywords Bioleaching . Genomics . Proteomics . extremophiles, including bacterial and archaeal species. In Metabolomics addition, extremophiles are also being studied to understand life in extreme conditions, and therefore, the study of proteo- mics and metabolomics will render the discovery of bio- markers used in the search for evidence of existing or past extra-terrestrial life (Bonnefoy and Holmes 2012). Extremophilic microorganisms have been isolated from min- * Roberto A. Bobadilla-Fazzini ing operations (Johnson et al. 2001; Okibe et al. 2003; Tyson [email protected] et al. 2004), and their role in the dynamics and evolution of minerals has been widely discussed (Santelli et al. 2009). 1 BioSigma ‘S.A.’, Parque Industrial Los Libertadores, Lote 106, These microorganisms, naturally present in the native flora Colina, Chile of minerals, are known to have a role in the 2 Biofilm Centre, Aquatische Biotechnologie, Universität biohydrometallurgical leaching processes, and their presence Duisburg-Essen, Universitätstraße 5, 45141 Essen, Germany hasbeenlinkedtoimprovedextractionofmetalsincluding Appl Microbiol Biotechnol copper, nickel, cobalt, zinc, and uranium. Bioleaching dumps classified as Ferroplasma cupricumulans (Hawkes et al. and heaps operating with this technology can be found in 2006) and later re-classified as Acidiplasma cupricumulans mines all over the world such as Radomiro Tomic (Chile), (Golyshina et al. 2009). Also, the identification of moderate Girilambone (Australia), Barberton (South Africa), Cerro thermophilic mixo- and/or heterotrophs from the Sulfobacillus Verde (Peru), Morenci (United States), Talvivaara (Finland), genus as the dominant population of the heap operation at the Sabetaung-Kyisintaung (Myanmar), and Dexing and Agnes Gold Mine in Barberton, South Africa (Coram-Uliana Zijinshan (China), among other mining sites. Therefore, omics et al. 2006), or the presence of chemolithoautotrophic iron- techniques have a unique worldwide-applied biotechnological oxidizing Leptospirilli in a tailings impoundment at the La niche to be impacted not only in terms of knowledge devel- Andina copper mine in Chile (Diaby et al. 2007). These studies, opment but also for biohydrometallurgical process design, among others, have shown the diversity of microbial popula- control, and optimization. tions in bioleaching operations. In our research group, we have In this mini-review, differing from others previously pub- used genomics information as the base for the development of lished (Cárdenas et al. 2010), we summarize the state of ge- patented techniques that allow an accurate monitoring of the nomics, proteomics, and metabolomics in the field of acido- microbial populations during the bioleaching process (Maass philes, emphasizing the current and future impacts of this et al. 2010;Paradaetal.2013; Ehrenfeld et al. 2012). Moreover, biotechnological knowledge in the development of spatial and temporal microbial population dynamics changes bioleaching at industrial scale. have been described within and during bioelaching stages (Remonsellez et al. 2009;Acostaetal.2014) and also depend- ing on the oxidation state of the minerals (Schippers et al. Current and future impacts of genomics 2010). In our opinion, the spatio-temporal analysis of acidophil- on bioleaching ic microbial populations during bioleaching is a major impact that (meta)-genomics will generate in the coming future. Re- Today, we have a completely different scenario compared cently, we have analyzed the microbial dynamics of lab-scale with the year 2000, when the first gapped genome sequence bioleaching of a mainly primary copper sulfide low-grade ore of Acidithiobacillus ferrooxidans (formerly Thiobacillus by massive sequencing technology using the MiSeq Illumina ferrooxidans and the archetype of a bioleaching microorgan- platform. Besides the prevalence of Acidithiobacillus and ism) was published (Selkov et al. 2000). Currently, 55 bacte- Sulfobacillus genera, the presence of anoxybacilli as relevant rial and 36 archaeal complete genomes from microorganisms members of the leaching microbial community has been iden- that are present in bioleaching processes are publicly available tified. Anoxybacillus spp., initially named as strict anaerobes, according to the NCBI database (see Table 1), and the tenden- includes aerobes, facultative anaerobes, and facultative aerobes cy to an exponential increase is evident (see Fig. 1). One main found in moderate- to high-temperature habitats such as geo- question is how the knowledge generated in these 15 years of thermalhotsprings(Gohetal.2014). Despite that this genus genomics of leaching microorganisms has contributed to im- has been characterized so far as alkaliphilic or alkali tolerant, provements in this field and particularly, which are and would our massive sequencing data has recently shown that up to be the major future impacts at industrial scale. 13 % of the acid-leaching population is composed of this genus Genomics has certainly made a major impact on our knowl- under the conditions tested (Bobadilla-Fazzini, unpublished edge of bioleaching. First of all, partial and full genome se- data). quencing has allowed the determination of the biodiversity Future impacts of genomics, by means of more compre- within leaching environments and the development of hensive, reliable, fast, and cheap next-generation sequencing molecular-based methods to scrutinize the temporal population technologies will lead to a better bioleaching operational de- dynamics of different bioleaching processes. For a long time, sign and control (Demergasso et al. 2010). Acidithiobacillus ferrooxidans was thought to be the most sig- A second major impact of genomics has been to provide nificant microorganism for metal sulfide bioleaching, however, information for the in silico reconstruction of metabolic capa- the advances in genomics knowledge together with the devel- bilities of formerly unknown essential aspects of bioleaching, opment of bioidentification molecular techniques such as such as the metabolic routes for iron and reduced inorganic DGGE, FISH, and quantitative PCR (qPCR) has driven the sulfur compounds (RISC) oxidation. Conceptual models based exploration of extreme mineral leaching environments for on genomics data have shown the intricate and alternative met- new microorganisms with potential commercial applications, abolic pathways for RISC compounds showing common fea- resulting in a more comprehensive understanding of the biodi- tures between Bacteria and Archaea (Chen et al. 2012), new versity of acidophilic environments. Interesting examples are metabolic characteristics, and environmental adaptation in the biodiversity obtained from heap solids and solutions col- Acidithiobacillus ferrooxidans and Leptospirillum ferriphilum lected from the Myanmar Ivanhoe Copper company, which (Levicán et al. 2008), Acidithiobacillus caldus (Mangold et al. showed the prevalence